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Title: Global analysis of truncated RNA ends reveals novel insights into ribosome stalling in plants      
keywords:
Transcriptome or Gene expression
ID:
PRJNA310776
description:
High-throughput approaches for profiling the 5' ends of RNA degradation intermediates on a genome-wide scale are frequently applied in the validation of cleavage sites guided by microRNAs (miRNAs). However, the complexity of the RNA degradome beyond miRNA targets is currently largely unclear which limits the application of RNA degradome. Here, we provide multiple lines of evidence to show that the plant RNA degradome contains in vivo ribosome-protected mRNA fragments. We observed a 3-nt periodicity and a bias toward the translational frame in the global analysis of 5' truncated mRNA ends mapped to the coding sequence (CDS) of Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa) and soybean (Glycine max). In addition, predominant 5' termini of RNA degradation intermediates separated by a length equal to a ribosome-protected mRNA fragment were evident in some conserved peptide upstream open reading frames (uORFs) of Arabidopsis and rice. Through the analysis of RNA degradome data, we uncovered novel uORFs and CDS regions potentially associated with stacked ribosomes in Arabidopsis. Furthermore, the analysis of RNA degradome data suggested that the binding of Arabidopsis ARGONAUTE7 to a non-cleavable target site of miR390 might directly hinder ribosome movement. This work demonstrates an alternative use of RNA degradome data in the study of ribosome stalling. Overall design: Profiling 5' ends of RNA degradation intermediate in Arabidopsis thaliana seedlings and inflorescences by parallel analysis of RNA ends (PARE)
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landingpage: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA310776
authentication:
none
authorization:
none
ID:
pmid:27742800
name:
Arabidopsis thaliana
ncbiID:
ncbitax:3702
abbreviation:
NCBI
homePage: http://www.ncbi.nlm.nih.gov
ID:
SCR:006472
name:
National Center for Biotechnology Information
homePage: http://www.ncbi.nlm.nih.gov/bioproject
ID:
SCR:004801
name:
NCBI BioProject